From 9b6a8cb8b92d48933190e2b2b017d69d3159be2c Mon Sep 17 00:00:00 2001 From: Adam Rauch Date: Mon, 25 May 2026 16:54:58 -0700 Subject: [PATCH] Update copyrights and licenses --- elisa/jest.config.js | 5 +++++ .../dbscripts/postgresql/elisa-0.000-23.000.sql | 2 +- .../dbscripts/sqlserver/elisa-0.000-23.000.sql | 2 +- elisa/resources/schemas/elisa.xml | 2 +- elisa/src/client/RunDetails/RunDetails.test.tsx | 5 +++++ elisa/src/client/RunDetails/RunDetails.tsx | 5 +++++ elisa/src/client/RunDetails/actions.ts | 5 +++++ elisa/src/client/RunDetails/app.tsx | 5 +++++ .../components/CalibrationCurvePanel.test.tsx | 5 +++++ .../components/CalibrationCurvePanel.tsx | 5 +++++ .../components/CurveFitDataDisplay.test.tsx | 5 +++++ .../RunDetails/components/CurveFitDataDisplay.tsx | 5 +++++ .../RunDetails/components/CurveFitPanel.test.tsx | 5 +++++ .../RunDetails/components/CurveFitPanel.tsx | 5 +++++ .../components/DataSelectionsPanel.test.tsx | 5 +++++ .../RunDetails/components/DataSelectionsPanel.tsx | 5 +++++ .../RunDetails/components/PlotButtonBar.test.tsx | 5 +++++ .../RunDetails/components/PlotButtonBar.tsx | 5 +++++ .../components/PlotOptionsPanel.test.tsx | 5 +++++ .../RunDetails/components/PlotOptionsPanel.tsx | 5 +++++ elisa/src/client/RunDetails/constants.ts | 5 +++++ elisa/src/client/RunDetails/dev.tsx | 5 +++++ elisa/src/client/RunDetails/models.ts | 5 +++++ elisa/src/client/RunDetails/utils.test.ts | 5 +++++ elisa/src/client/RunDetails/utils.ts | 5 +++++ elisa/src/client/entryPoints.js | 2 +- .../labkey/elisa/AbstractElisaImportHelper.java | 15 +++++++++++++++ .../src/org/labkey/elisa/ElisaAssayProvider.java | 2 +- .../org/labkey/elisa/ElisaContainerListener.java | 15 +++++++++++++++ elisa/src/org/labkey/elisa/ElisaController.java | 2 +- elisa/src/org/labkey/elisa/ElisaDataHandler.java | 2 +- elisa/src/org/labkey/elisa/ElisaImportHelper.java | 15 +++++++++++++++ elisa/src/org/labkey/elisa/ElisaModule.java | 2 +- .../org/labkey/elisa/ElisaPlateLayoutHandler.java | 2 +- .../src/org/labkey/elisa/ElisaProtocolSchema.java | 2 +- .../src/org/labkey/elisa/ElisaProviderSchema.java | 15 +++++++++++++++ .../elisa/ElisaSampleFilePropertyHelper.java | 15 +++++++++++++++ .../labkey/elisa/HighThroughputImportHelper.java | 15 +++++++++++++++ .../src/org/labkey/elisa/ManualImportHelper.java | 15 +++++++++++++++ .../labkey/elisa/actions/ElisaRunUploadForm.java | 2 +- .../elisa/actions/ElisaUploadWizardAction.java | 2 +- .../actions/PlateConcentrationPropertyHelper.java | 2 +- .../org/labkey/elisa/plate/BioTekPlateReader.java | 2 +- elisa/src/org/labkey/elisa/query/CurveFitDb.java | 15 +++++++++++++++ .../src/org/labkey/elisa/query/CurveFitTable.java | 15 +++++++++++++++ .../src/org/labkey/elisa/query/ElisaManager.java | 15 +++++++++++++++ .../org/labkey/elisa/query/ElisaResultsTable.java | 2 +- .../src/org/labkey/elisa/view/runDetailsView.jsp | 2 +- elisa/test/js/setup.ts | 5 +++++ .../dbscripts/postgresql/elispotlk-0.00-18.30.sql | 2 +- .../postgresql/elispotlk-25.000-25.001.sql | 2 +- .../dbscripts/sqlserver/elispotlk-0.00-18.30.sql | 2 +- .../sqlserver/elispotlk-25.000-25.001.sql | 2 +- elispotassay/resources/schemas/elispotlk.xml | 2 +- .../elispot/AbstractElispotDataHandler.java | 2 +- .../org/labkey/elispot/ElispotAssayProvider.java | 2 +- .../src/org/labkey/elispot/ElispotController.java | 2 +- .../elispot/ElispotDataExchangeHandler.java | 2 +- .../org/labkey/elispot/ElispotDataHandler.java | 2 +- .../src/org/labkey/elispot/ElispotManager.java | 2 +- .../src/org/labkey/elispot/ElispotModule.java | 2 +- .../labkey/elispot/ElispotPlateLayoutHandler.java | 2 +- .../org/labkey/elispot/ElispotProtocolSchema.java | 2 +- .../org/labkey/elispot/ElispotProviderSchema.java | 2 +- .../org/labkey/elispot/ElispotRunUploadForm.java | 2 +- .../labkey/elispot/ElispotUploadWizardAction.java | 2 +- .../elispot/PlateAnalytePropertyHelper.java | 2 +- .../elispot/PlateAntigenPropertyHelper.java | 2 +- .../src/org/labkey/elispot/RunDataRow.java | 2 +- .../pipeline/BackgroundSubtractionJob.java | 2 +- .../org/labkey/elispot/plate/AIDPlateReader.java | 2 +- .../elispot/plate/FluorescentPlateInfo.java | 2 +- .../src/org/labkey/elispot/plate/PlateInfo.java | 2 +- .../query/ElispotAntigenCrosstabTable.java | 2 +- .../elispot/query/ElispotAntigenDomainKind.java | 2 +- .../elispot/query/ElispotRunAntigenTable.java | 2 +- .../labkey/elispot/query/ElispotRunDataTable.java | 2 +- .../query/PlateBasedAssayRunDataTable.java | 2 +- .../src/org/labkey/elispot/view/plateSummary.jsp | 2 +- elispotassay/webapp/elispot/PlateSummary.js | 2 +- flow/enginesrc/org/labkey/flow/Main.java | 2 +- .../flow/analysis/chart/DataFrameXYDataset.java | 2 +- .../flow/analysis/chart/DatasetFactory.java | 2 +- .../flow/analysis/chart/DensityColorBar.java | 2 +- .../flow/analysis/chart/DensityColorPalette.java | 2 +- .../flow/analysis/chart/DensityDataset.java | 2 +- .../labkey/flow/analysis/chart/DensityPlot.java | 2 +- .../flow/analysis/chart/FlowLinearAxis.java | 15 +++++++++++++++ .../flow/analysis/chart/FlowLogarithmicAxis.java | 2 +- .../labkey/flow/analysis/chart/HistDataset.java | 2 +- .../org/labkey/flow/analysis/chart/HistPlot.java | 2 +- .../labkey/flow/analysis/chart/PlotFactory.java | 2 +- .../analysis/data/ConstrainedNumberArray.java | 2 +- .../labkey/flow/analysis/data/DoubleArray.java | 2 +- .../org/labkey/flow/analysis/data/FloatArray.java | 2 +- .../org/labkey/flow/analysis/data/IntArray.java | 2 +- .../labkey/flow/analysis/data/NumberArray.java | 2 +- .../flow/analysis/data/SubsetNumberArray.java | 2 +- .../org/labkey/flow/analysis/model/Analysis.java | 2 +- .../org/labkey/flow/analysis/model/AndGate.java | 2 +- .../analysis/model/AutoCompensationScript.java | 2 +- .../labkey/flow/analysis/model/BaseWorkspace.java | 2 +- .../flow/analysis/model/CalibrationTable.java | 2 +- .../model/CleanNameExpressionTransform.java | 2 +- .../analysis/model/CompensationCalculation.java | 2 +- .../flow/analysis/model/CompensationMatrix.java | 2 +- .../org/labkey/flow/analysis/model/DataFrame.java | 2 +- .../labkey/flow/analysis/model/EllipseGate.java | 2 +- .../flow/analysis/model/ExternalAnalysis.java | 2 +- .../org/labkey/flow/analysis/model/FCS.java | 2 +- .../org/labkey/flow/analysis/model/FCSCache.java | 2 +- .../org/labkey/flow/analysis/model/FCSHeader.java | 2 +- .../flow/analysis/model/FCSKeywordData.java | 2 +- .../analysis/model/FixedCalibrationTable.java | 2 +- .../labkey/flow/analysis/model/FlowException.java | 2 +- .../analysis/model/FlowJo10_0_6Workspace.java | 2 +- .../flow/analysis/model/FlowJoWorkspace.java | 2 +- .../org/labkey/flow/analysis/model/Gate.java | 2 +- .../org/labkey/flow/analysis/model/GateList.java | 2 +- .../labkey/flow/analysis/model/ISampleInfo.java | 2 +- .../labkey/flow/analysis/model/IWorkspace.java | 2 +- .../analysis/model/IdentityCalibrationTable.java | 2 +- .../labkey/flow/analysis/model/IntervalGate.java | 2 +- .../labkey/flow/analysis/model/Mac2Workspace.java | 2 +- .../labkey/flow/analysis/model/MacWorkspace.java | 2 +- .../flow/analysis/model/MinMaxConstraint.java | 2 +- .../org/labkey/flow/analysis/model/NotGate.java | 2 +- .../org/labkey/flow/analysis/model/OrGate.java | 2 +- .../labkey/flow/analysis/model/PC75Workspace.java | 2 +- .../labkey/flow/analysis/model/PCWorkspace.java | 2 +- .../labkey/flow/analysis/model/ParameterInfo.java | 2 +- .../org/labkey/flow/analysis/model/Polygon.java | 2 +- .../labkey/flow/analysis/model/PolygonGate.java | 2 +- .../labkey/flow/analysis/model/Population.java | 2 +- .../flow/analysis/model/PopulationName.java | 2 +- .../labkey/flow/analysis/model/PopulationSet.java | 2 +- .../labkey/flow/analysis/model/RegionGate.java | 2 +- .../flow/analysis/model/SampleCriteria.java | 2 +- .../labkey/flow/analysis/model/SampleIdMap.java | 2 +- .../flow/analysis/model/SampleInfoBase.java | 2 +- .../flow/analysis/model/ScalingFunction.java | 2 +- .../flow/analysis/model/ScriptComponent.java | 2 +- .../flow/analysis/model/ScriptSettings.java | 2 +- .../labkey/flow/analysis/model/StatisticSet.java | 2 +- .../labkey/flow/analysis/model/StatsTable.java | 2 +- .../org/labkey/flow/analysis/model/Subset.java | 2 +- .../flow/analysis/model/SubsetExpressionGate.java | 2 +- .../labkey/flow/analysis/model/SubsetPart.java | 2 +- .../flow/analysis/model/ValueConstraint.java | 2 +- .../org/labkey/flow/analysis/model/Workspace.java | 2 +- .../flow/analysis/model/WorkspaceParser.java | 2 +- .../flow/analysis/util/AbstractRangeFunction.java | 15 +++++++++++++++ .../flow/analysis/util/LinearRangeFunction.java | 15 +++++++++++++++ .../flow/analysis/util/LogRangeFunction.java | 2 +- .../flow/analysis/util/LogicleRangeFunction.java | 15 +++++++++++++++ .../labkey/flow/analysis/util/RangeFunction.java | 2 +- .../analysis/util/SimpleLogRangeFunction.java | 2 +- .../org/labkey/flow/analysis/web/ChannelData.java | 2 +- .../org/labkey/flow/analysis/web/ChannelKey.java | 2 +- .../org/labkey/flow/analysis/web/CompHandler.java | 2 +- .../org/labkey/flow/analysis/web/CompSign.java | 2 +- .../flow/analysis/web/CompensationResult.java | 2 +- .../org/labkey/flow/analysis/web/FCSAnalyzer.java | 2 +- .../org/labkey/flow/analysis/web/FCSRef.java | 2 +- .../org/labkey/flow/analysis/web/FCSViewer.java | 2 +- .../org/labkey/flow/analysis/web/GraphSpec.java | 2 +- .../org/labkey/flow/analysis/web/PlotInfo.java | 2 +- .../org/labkey/flow/analysis/web/PlotTests.java | 2 +- .../labkey/flow/analysis/web/ScriptAnalyzer.java | 2 +- .../org/labkey/flow/analysis/web/SpecBase.java | 15 +++++++++++++++ .../labkey/flow/analysis/web/StatisticSpec.java | 2 +- .../flow/analysis/web/SubsetExpression.java | 2 +- .../labkey/flow/analysis/web/SubsetParser.java | 2 +- .../org/labkey/flow/analysis/web/SubsetSpec.java | 2 +- .../labkey/flow/persist/AnalysisSerializer.java | 2 +- .../org/labkey/flow/persist/AttributeSet.java | 2 +- .../org/labkey/flow/persist/InputRole.java | 2 +- .../org/labkey/flow/persist/ObjectType.java | 2 +- .../org/labkey/flow/util/KeywordUtil.java | 2 +- flow/resources/flowReports/qc.R | 2 +- .../dbscripts/postgresql/flow-0.000-22.000.sql | 2 +- .../dbscripts/sqlserver/flow-0.000-22.000.sql | 2 +- flow/resources/schemas/flow.xml | 2 +- .../web/Flow/editCompensationCalculation.js | 2 +- flow/resources/web/Flow/flowReport.js | 2 +- flow/resources/web/Flow/util.js | 2 +- flow/src/org/labkey/flow/FlowModule.java | 2 +- flow/src/org/labkey/flow/FlowPreference.java | 2 +- flow/src/org/labkey/flow/FlowServiceImpl.java | 2 +- flow/src/org/labkey/flow/FlowSettings.java | 2 +- flow/src/org/labkey/flow/ScriptParser.java | 2 +- .../flow/controllers/BaseFlowController.java | 2 +- .../labkey/flow/controllers/FlowController.java | 2 +- .../org/labkey/flow/controllers/FlowParam.java | 2 +- .../flow/controllers/ReportsController.java | 2 +- .../labkey/flow/controllers/WorkspaceData.java | 2 +- .../labkey/flow/controllers/ajaxExecuteReport.jsp | 2 +- .../attribute/AttributeController.java | 2 +- .../flow/controllers/attribute/createAlias.jsp | 2 +- .../labkey/flow/controllers/attribute/details.jsp | 2 +- .../labkey/flow/controllers/attribute/edit.jsp | 2 +- .../labkey/flow/controllers/attribute/summary.jsp | 2 +- .../compensation/CompensationController.java | 2 +- .../controllers/compensation/showCompensation.jsp | 2 +- .../flow/controllers/compensation/upload.jsp | 2 +- .../org/labkey/flow/controllers/copyReport.jsp | 2 +- .../editscript/CompensationCalculationPage.java | 2 +- .../EditCompensationCalculationForm.java | 2 +- .../controllers/editscript/EditScriptForm.java | 2 +- .../controllers/editscript/EditSettingsForm.java | 2 +- .../controllers/editscript/ScriptController.java | 2 +- .../editscript/UploadAnalysisForm.java | 2 +- .../editscript/chooseCompensationRun.jsp | 2 +- .../labkey/flow/controllers/editscript/copy.jsp | 2 +- .../flow/controllers/editscript/editAnalysis.jsp | 2 +- .../editscript/editCompensationCalculation.jsp | 2 +- .../flow/controllers/editscript/editGateTree.jsp | 2 +- .../flow/controllers/editscript/editScript.jsp | 2 +- .../flow/controllers/editscript/editSettings.jsp | 2 +- .../editscript/showCompensationCalculation.jsp | 2 +- .../controllers/editscript/uploadAnalysis.jsp | 2 +- .../editscript/uploadCompensationCalculation.jsp | 2 +- .../controllers/executescript/AnalysisEngine.java | 2 +- .../executescript/AnalysisScriptController.java | 2 +- .../executescript/ChooseRunsRegion.java | 2 +- .../executescript/ChooseRunsToAnalyzeForm.java | 2 +- .../controllers/executescript/ChooseRunsView.java | 2 +- .../executescript/ImportAnalysisForm.java | 2 +- .../executescript/SamplesConfirmGridView.java | 2 +- .../controllers/executescript/ScriptOverview.java | 2 +- .../executescript/SelectedSamples.java | 2 +- 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.../flow/controllers/protocol/showSamples2.jsp | 2 +- .../flow/controllers/protocol/updateSamples.jsp | 2 +- flow/src/org/labkey/flow/controllers/reports.jsp | 2 +- .../flow/controllers/run/RunController.java | 2 +- .../org/labkey/flow/controllers/run/RunForm.java | 2 +- .../org/labkey/flow/controllers/run/RunsForm.java | 2 +- .../flow/controllers/run/StatusJsonHelper.java | 2 +- .../org/labkey/flow/controllers/run/download.jsp | 2 +- .../org/labkey/flow/controllers/run/showRun.jsp | 2 +- .../org/labkey/flow/controllers/selectReport.jsp | 2 +- .../flow/controllers/well/ChooseGraphForm.java | 2 +- .../flow/controllers/well/EditWellForm.java | 2 +- .../controllers/well/GraphContextualRoles.java | 2 +- .../flow/controllers/well/WellController.java | 2 +- .../labkey/flow/controllers/well/bulkUpdate.jsp | 2 +- .../labkey/flow/controllers/well/chooseGraph.jsp | 2 +- .../org/labkey/flow/controllers/well/editWell.jsp | 2 +- .../org/labkey/flow/controllers/well/showWell.jsp | 2 +- .../org/labkey/flow/data/FieldSubstitution.java | 2 +- .../org/labkey/flow/data/FlowAssayProvider.java | 2 +- .../labkey/flow/data/FlowCompensationControl.java | 2 +- .../labkey/flow/data/FlowCompensationMatrix.java | 2 +- flow/src/org/labkey/flow/data/FlowDataObject.java | 2 +- flow/src/org/labkey/flow/data/FlowDataType.java | 2 +- flow/src/org/labkey/flow/data/FlowExperiment.java | 2 +- .../src/org/labkey/flow/data/FlowFCSAnalysis.java | 2 +- flow/src/org/labkey/flow/data/FlowFCSFile.java | 2 +- flow/src/org/labkey/flow/data/FlowObject.java | 2 +- flow/src/org/labkey/flow/data/FlowProperty.java | 2 +- flow/src/org/labkey/flow/data/FlowProtocol.java | 2 +- .../flow/data/FlowProtocolImplementation.java | 2 +- .../org/labkey/flow/data/FlowProtocolSchema.java | 2 +- .../org/labkey/flow/data/FlowProtocolStep.java | 2 +- .../org/labkey/flow/data/FlowProviderSchema.java | 2 +- flow/src/org/labkey/flow/data/FlowRun.java | 2 +- .../org/labkey/flow/data/FlowRunWorkspace.java | 2 +- 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flow/src/org/labkey/flow/script/WorkspaceJob.java | 2 +- flow/src/org/labkey/flow/util/SampleUtil.java | 2 +- .../labkey/flow/view/ExportAnalysisManifest.java | 2 +- flow/src/org/labkey/flow/view/FlowQueryView.java | 2 +- flow/src/org/labkey/flow/view/GraphColumn.java | 2 +- .../src/org/labkey/flow/view/GraphDataRegion.java | 2 +- .../org/labkey/flow/view/SetGraphSizeView.java | 15 +++++++++++++++ flow/src/org/labkey/flow/view/exportAnalysis.jsp | 2 +- flow/src/org/labkey/flow/view/setComment.jsp | 2 +- flow/src/org/labkey/flow/view/setGraphSize.jsp | 2 +- .../org/labkey/flow/webparts/AnalysesWebPart.java | 2 +- .../flow/webparts/AnalysisScriptTypeColumn.java | 2 +- .../flow/webparts/AnalysisScriptsWebPart.java | 2 +- .../org/labkey/flow/webparts/FlowFolderType.java | 2 +- .../org/labkey/flow/webparts/FlowOverview.java | 2 +- flow/src/org/labkey/flow/webparts/FlowSummary.jsp | 2 +- .../labkey/flow/webparts/FlowSummaryWebPart.java | 2 +- .../org/labkey/flow/webparts/OverviewWebPart.java | 2 +- .../dbscripts/postgresql/luminex-0.000-23.000.sql | 2 +- .../postgresql/luminex-25.000-25.001.sql | 5 +++++ .../dbscripts/sqlserver/luminex-0.000-23.000.sql | 2 +- .../dbscripts/sqlserver/luminex-25.000-25.001.sql | 5 +++++ luminex/resources/schemas/luminex.xml | 2 +- .../transformscripts/labkey_luminex_transform.R | 2 +- .../AbstractLuminexControlUpdateService.java | 2 +- .../luminex/AnalyteDefaultValueService.java | 2 +- .../org/labkey/luminex/AnalyteImportHelper.java | 2 +- .../org/labkey/luminex/LeveyJenningsMenuView.java | 2 +- .../labkey/luminex/LuminexAnalyteDomainKind.java | 2 +- .../org/labkey/luminex/LuminexAssayProvider.java | 2 +- .../src/org/labkey/luminex/LuminexController.java | 2 +- .../org/labkey/luminex/LuminexDataDomainKind.java | 2 +- .../luminex/LuminexDataExchangeHandler.java | 2 +- .../org/labkey/luminex/LuminexDataHandler.java | 2 +- .../org/labkey/luminex/LuminexExcelParser.java | 2 +- .../luminex/LuminexExclusionPipelineJob.java | 2 +- .../org/labkey/luminex/LuminexImportHelper.java | 2 +- .../src/org/labkey/luminex/LuminexManager.java | 2 +- luminex/src/org/labkey/luminex/LuminexModule.java | 2 +- .../org/labkey/luminex/LuminexOORIndicator.java | 2 +- .../src/org/labkey/luminex/LuminexReplicate.java | 2 +- .../labkey/luminex/LuminexResultsDataRegion.java | 2 +- .../labkey/luminex/LuminexRunAsyncContext.java | 2 +- .../src/org/labkey/luminex/LuminexRunContext.java | 2 +- .../src/org/labkey/luminex/LuminexRunCreator.java | 2 +- .../labkey/luminex/LuminexRunDatabaseContext.java | 2 +- .../org/labkey/luminex/LuminexRunUploadForm.java | 2 +- .../labkey/luminex/LuminexSaveExclusionsForm.java | 2 +- .../luminex/LuminexSingleExclusionCommand.java | 2 +- .../labkey/luminex/LuminexUnitTestContext.java | 2 +- .../org/labkey/luminex/LuminexUpgradeCode.java | 15 +++++++++++++++ .../labkey/luminex/LuminexUploadWizardAction.java | 2 +- .../luminex/model/AbstractAnalyteQCFlag.java | 2 +- .../luminex/model/AbstractLuminexControl.java | 2 +- .../model/AbstractLuminexControlAnalyte.java | 2 +- luminex/src/org/labkey/luminex/model/Analyte.java | 2 +- .../luminex/model/AnalyteSinglePointControl.java | 2 +- .../model/AnalyteSinglePointControlQCFlag.java | 2 +- .../labkey/luminex/model/AnalyteTitration.java | 2 +- .../luminex/model/AnalyteTitrationQCFlag.java | 2 +- .../src/org/labkey/luminex/model/CVQCFlag.java | 2 +- .../src/org/labkey/luminex/model/CurveFit.java | 2 +- .../src/org/labkey/luminex/model/GuideSet.java | 2 +- .../org/labkey/luminex/model/LuminexDataRow.java | 2 +- .../src/org/labkey/luminex/model/LuminexWell.java | 2 +- .../labkey/luminex/model/LuminexWellGroup.java | 2 +- .../labkey/luminex/model/SinglePointControl.java | 2 +- .../src/org/labkey/luminex/model/Titration.java | 2 +- .../luminex/query/AbstractCurveFitPivotTable.java | 2 +- .../luminex/query/AbstractExclusionTable.java | 2 +- .../luminex/query/AbstractLuminexTable.java | 2 +- .../query/AnalytePropStandardsDisplayColumn.java | 2 +- .../query/AnalyteSinglePointControlTable.java | 2 +- .../org/labkey/luminex/query/AnalyteTable.java | 2 +- .../luminex/query/AnalyteTitrationTable.java | 2 +- .../org/labkey/luminex/query/CurveFitTable.java | 2 +- .../luminex/query/ExclusionUIDisplayColumn.java | 2 +- .../luminex/query/GuideSetCurveFitTable.java | 2 +- .../org/labkey/luminex/query/GuideSetTable.java | 2 +- .../labkey/luminex/query/LuminexDataTable.java | 2 +- .../luminex/query/LuminexProtocolSchema.java | 2 +- .../query/NegativeBeadDisplayColumnFactory.java | 2 +- .../query/NegativeBeadDisplayColumnGroup.java | 2 +- .../query/QCFlagHighlightDisplayColumn.java | 2 +- .../labkey/luminex/query/RunExclusionTable.java | 2 +- .../luminex/query/SinglePointControlTable.java | 2 +- .../org/labkey/luminex/query/TitrationTable.java | 2 +- .../labkey/luminex/query/WellExclusionTable.java | 2 +- .../src/org/labkey/luminex/view/defaultValues.jsp | 2 +- .../org/labkey/luminex/view/exclusionWarning.jsp | 2 +- .../labkey/luminex/view/guideSetConfirmDelete.jsp | 2 +- .../org/labkey/luminex/view/leveyJenningsMenu.jsp | 2 +- .../labkey/luminex/view/leveyJenningsReport.jsp | 2 +- .../labkey/luminex/view/titrationWellRoles.jsp | 2 +- .../dialogs/SinglepointExclusionDialog.java | 2 +- .../importwizard/AnalytePropertiesWebPart.java | 2 +- .../importwizard/BatchPropertiesWebPart.java | 2 +- .../importwizard/DefineWellRoleWebPart.java | 2 +- .../importwizard/RunPropertiesWebPart.java | 2 +- .../test/pages/luminex/ExclusionReportPage.java | 2 +- .../pages/luminex/LeveyJenningsPlotWindow.java | 2 +- .../test/pages/luminex/LuminexImportWizard.java | 2 +- .../luminex/SetAnalyteDefaultValuesPage.java | 2 +- .../tests/luminex/LuminexAsyncImportTest.java | 2 +- .../test/tests/luminex/LuminexEC50Test.java | 2 +- .../tests/luminex/LuminexExcludableWellsTest.java | 2 +- .../luminex/LuminexExcludedTitrationTest.java | 2 +- .../luminex/LuminexExclusionRetentionTest.java | 2 +- .../luminex/LuminexGuideSetDisablingTest.java | 2 +- .../test/tests/luminex/LuminexGuideSetTest.java | 2 +- .../tests/luminex/LuminexJavaTransformTest.java | 2 +- .../tests/luminex/LuminexMultipleCurvesTest.java | 2 +- .../test/tests/luminex/LuminexPositivityTest.java | 2 +- .../test/tests/luminex/LuminexRTransformTest.java | 2 +- .../tests/luminex/LuminexSinglePointTest.java | 2 +- .../labkey/test/tests/luminex/LuminexTest.java | 2 +- .../tests/luminex/LuminexUploadAndLinkTest.java | 2 +- .../luminex/LuminexValueBasedGuideSetTest.java | 2 +- .../test/util/luminex/LuminexGuideSetHelper.java | 2 +- luminex/webapp/luminex/ApplyGuideSetPanel.js | 2 +- luminex/webapp/luminex/GuideSetWindow.js | 2 +- .../luminex/LeveyJenningsGraphParamsPanel.js | 2 +- .../webapp/luminex/LeveyJenningsGuideSetPanel.js | 2 +- .../webapp/luminex/LeveyJenningsPlotHelpers.js | 2 +- .../luminex/LeveyJenningsTrackingDataPanel.js | 2 +- .../webapp/luminex/LeveyJenningsTrendPlotPanel.js | 2 +- luminex/webapp/luminex/ManageGuideSetPanel.js | 2 +- luminex/webapp/luminex/NegativeBeadPopulation.js | 2 +- .../luminex/exclusion/AnalyteExclusionPanel.js | 2 +- .../luminex/exclusion/BaseExclusionPanel.js | 2 +- .../exclusion/SinglepointUnknownExclusionPanel.js | 2 +- .../luminex/exclusion/TitrationExclusionPanel.js | 2 +- .../luminex/exclusion/WellExclusionPanel.js | 2 +- .../postgresql/microarray-0.000-21.000.sql | 2 +- microarray/resources/schemas/microarray.xml | 2 +- microarray/resources/web/microarray/geo_export.js | 2 +- .../assay/matrix/AbstractMatrixRunCreator.java | 2 +- .../microarray/MicroarrayContainerListener.java | 2 +- .../org/labkey/microarray/MicroarrayManager.java | 2 +- .../org/labkey/microarray/MicroarrayModule.java | 2 +- .../FeatureAnnotationSetController.java | 2 +- .../matrix/ExpressionMatrixAssayProvider.java | 2 +- .../matrix/ExpressionMatrixDataHandler.java | 2 +- .../ExpressionMatrixExperimentListener.java | 2 +- .../matrix/ExpressionMatrixProtocolSchema.java | 2 +- .../matrix/ExpressionMatrixRunCreator.java | 2 +- .../microarray/matrix/FeatureDataTable.java | 2 +- .../query/FeatureAnnotationSetTable.java | 2 +- .../microarray/query/MicroarrayUserSchema.java | 2 +- .../view/FeatureAnnotationSetQueryView.java | 2 +- .../microarray/view/uploadFeatureAnnotation.jsp | 2 +- .../org/labkey/api/util/massSpecDataFileType.java | 2 +- .../dbscripts/postgresql/ms2-0.000-21.000.sql | 2 +- .../dbscripts/postgresql/ms2-25.000-25.001.sql | 5 +++++ .../schemas/dbscripts/postgresql/ms2-create.sql | 2 +- .../schemas/dbscripts/postgresql/ms2-drop.sql | 2 +- .../dbscripts/sqlserver/ms2-0.000-21.000.sql | 2 +- .../dbscripts/sqlserver/ms2-25.000-25.001.sql | 5 +++++ .../schemas/dbscripts/sqlserver/ms2-create.sql | 2 +- .../schemas/dbscripts/sqlserver/ms2-drop.sql | 2 +- ms2/resources/schemas/ms2.xml | 2 +- .../labkey/ms2/AbstractPeptideDisplayColumn.java | 2 +- .../labkey/ms2/AbstractTextSpectrumRenderer.java | 2 +- .../labkey/ms2/BibliospecSpectrumRenderer.java | 2 +- ms2/src/org/labkey/ms2/CumulativeTimer.java | 2 +- ms2/src/org/labkey/ms2/DeltaScanColumn.java | 2 +- ms2/src/org/labkey/ms2/DtaSpectrumRenderer.java | 2 +- .../org/labkey/ms2/EditElutionGraphContext.java | 2 +- ms2/src/org/labkey/ms2/ElutionGraph.java | 2 +- ms2/src/org/labkey/ms2/ErrorImageRenderer.java | 2 +- .../org/labkey/ms2/GroupNumberDisplayColumn.java | 2 +- ms2/src/org/labkey/ms2/Hydrophobicity3.java | 5 ----- ms2/src/org/labkey/ms2/HydrophobicityColumn.java | 2 +- .../org/labkey/ms2/IcatProteinQuantitation.java | 2 +- ms2/src/org/labkey/ms2/MS2ContainerListener.java | 15 +++++++++++++++ ms2/src/org/labkey/ms2/MS2Controller.java | 2 +- ms2/src/org/labkey/ms2/MS2ExportType.java | 2 +- ms2/src/org/labkey/ms2/MS2FolderType.java | 2 +- ms2/src/org/labkey/ms2/MS2Fraction.java | 2 +- ms2/src/org/labkey/ms2/MS2GZFileRenderer.java | 2 +- ms2/src/org/labkey/ms2/MS2Importer.java | 2 +- ms2/src/org/labkey/ms2/MS2Manager.java | 2 +- ms2/src/org/labkey/ms2/MS2Module.java | 2 +- ms2/src/org/labkey/ms2/MS2Peptide.java | 2 +- ms2/src/org/labkey/ms2/MS2Run.java | 2 +- ms2/src/org/labkey/ms2/MS2RunType.java | 2 +- .../labkey/ms2/MS2SearchExperimentRunType.java | 2 +- ms2/src/org/labkey/ms2/MS2ServiceImpl.java | 2 +- .../ms2/MascotDatExperimentDataHandler.java | 2 +- ms2/src/org/labkey/ms2/MascotDatImporter.java | 2 +- .../labkey/ms2/PepXmlExperimentDataHandler.java | 2 +- ms2/src/org/labkey/ms2/PepXmlImporter.java | 2 +- ms2/src/org/labkey/ms2/PeptideImporter.java | 2 +- ms2/src/org/labkey/ms2/PeptideManager.java | 15 +++++++++++++++ ms2/src/org/labkey/ms2/PeptideProphetGraphs.java | 2 +- ms2/src/org/labkey/ms2/PeptideQuantitation.java | 2 +- ms2/src/org/labkey/ms2/PklSpectrumRenderer.java | 2 +- .../org/labkey/ms2/ProteinCoverageMapBuilder.java | 2 +- ms2/src/org/labkey/ms2/ProteinDisplayColumn.java | 2 +- ms2/src/org/labkey/ms2/ProteinGroupProteins.java | 2 +- .../labkey/ms2/ProteinGroupWithQuantitation.java | 2 +- .../org/labkey/ms2/ProteinListDisplayColumn.java | 2 +- .../ms2/ProteinProphetExperimentDataHandler.java | 2 +- .../org/labkey/ms2/ProteinProphetImporter.java | 2 +- ms2/src/org/labkey/ms2/RunListCache.java | 2 +- ms2/src/org/labkey/ms2/RunListException.java | 2 +- ms2/src/org/labkey/ms2/ShowPeptideContext.java | 2 +- ms2/src/org/labkey/ms2/SpectrumImporter.java | 2 +- ms2/src/org/labkey/ms2/SpectrumIterator.java | 2 +- ms2/src/org/labkey/ms2/SpectrumRenderer.java | 2 +- ms2/src/org/labkey/ms2/blastAdmin.jsp | 2 +- .../org/labkey/ms2/compare/CompareDataRegion.java | 2 +- .../labkey/ms2/compare/CompareExcelWriter.java | 2 +- ms2/src/org/labkey/ms2/compare/CompareQuery.java | 2 +- .../labkey/ms2/compare/MS2ReportUIProvider.java | 2 +- ms2/src/org/labkey/ms2/compare/RunColumn.java | 2 +- .../labkey/ms2/compare/SpectraCountQueryView.java | 2 +- .../labkey/ms2/compare/SpectraCountRReport.java | 2 +- .../ms2/compare/comparePeptideQueryOptions.jsp | 2 +- .../compare/compareProteinProphetQueryOptions.jsp | 2 +- .../compare/compareSearchEngineProteinOptions.jsp | 2 +- .../labkey/ms2/compare/spectraCountOptions.jsp | 2 +- ms2/src/org/labkey/ms2/currentFilter.jsp | 2 +- ms2/src/org/labkey/ms2/decoySummary.jsp | 2 +- ms2/src/org/labkey/ms2/editElution.jsp | 2 +- ms2/src/org/labkey/ms2/extraExportOptions.jsp | 2 +- ms2/src/org/labkey/ms2/filterHeader.jsp | 2 +- ms2/src/org/labkey/ms2/manageViews.jsp | 2 +- ms2/src/org/labkey/ms2/mascotConfig.jsp | 2 +- ms2/src/org/labkey/ms2/ms2Admin.jsp | 2 +- ms2/src/org/labkey/ms2/peptideChart.jsp | 2 +- .../ms2/peptideview/AbstractMS2RunView.java | 2 +- .../org/labkey/ms2/peptideview/MS2ResultSet.java | 2 +- .../labkey/ms2/peptideview/MS2RunViewType.java | 2 +- .../org/labkey/ms2/peptideview/PeptidesView.java | 2 +- .../peptideview/ProteinDisplayColumnFactory.java | 2 +- .../ms2/peptideview/ProteinStringExpression.java | 2 +- .../ms2/peptideview/QueryPeptideMS2RunView.java | 2 +- .../peptideview/QueryProteinGroupMS2RunView.java | 2 +- .../QueryResultSetSpectrumIterator.java | 2 +- .../peptideview/ResultSetSpectrumIterator.java | 2 +- .../ms2/peptideview/SingleMS2RunRReport.java | 2 +- ms2/src/org/labkey/ms2/pickView.jsp | 2 +- .../ms2/pipeline/AbstractMS2PipelineProvider.java | 2 +- .../pipeline/AbstractMS2SearchPipelineJob.java | 2 +- .../AbstractMS2SearchPipelineProvider.java | 2 +- .../ms2/pipeline/AbstractMS2SearchProtocol.java | 2 +- .../AbstractMS2SearchProtocolFactory.java | 2 +- .../ms2/pipeline/AbstractMS2SearchTask.java | 2 +- .../pipeline/AbstractMS2SearchTaskFactory.java | 2 +- .../labkey/ms2/pipeline/ConfigureSequenceDB.jsp | 2 +- .../org/labkey/ms2/pipeline/FastaCheckTask.java | 2 +- .../pipeline/FastaCheckTaskFactorySettings.java | 2 +- .../labkey/ms2/pipeline/LibraProtocolFactory.java | 2 +- .../labkey/ms2/pipeline/MS2ImportPipelineJob.java | 2 +- .../ms2/pipeline/MS2PipelineJobSupport.java | 2 +- .../labkey/ms2/pipeline/MS2PipelineManager.java | 2 +- .../labkey/ms2/pipeline/MS2PipelineProvider.java | 2 +- .../org/labkey/ms2/pipeline/MS2SearchForm.java | 2 +- .../labkey/ms2/pipeline/MS2SearchJobSupport.java | 2 +- .../org/labkey/ms2/pipeline/ParameterNames.java | 15 +++++++++++++++ .../labkey/ms2/pipeline/PipelineController.java | 2 +- .../ms2/pipeline/ProteinProphetPipelineJob.java | 2 +- .../pipeline/ProteinProphetPipelineProvider.java | 2 +- .../ms2/pipeline/QuantitationAlgorithm.java | 2 +- ms2/src/org/labkey/ms2/pipeline/SearchClient.java | 2 +- ms2/src/org/labkey/ms2/pipeline/Sqt2PinTask.java | 2 +- ms2/src/org/labkey/ms2/pipeline/TPPTask.java | 2 +- .../org/labkey/ms2/pipeline/UnknownMS2Run.java | 2 +- .../pipeline/comet/Comet2014ParamsBuilder.java | 2 +- .../pipeline/comet/Comet2015ParamsBuilder.java | 2 +- .../labkey/ms2/pipeline/comet/CometParams.java | 2 +- .../ms2/pipeline/comet/CometPipelineJob.java | 2 +- .../ms2/pipeline/comet/CometPipelineProvider.java | 2 +- .../org/labkey/ms2/pipeline/comet/CometRun.java | 2 +- .../ms2/pipeline/comet/CometSearchProtocol.java | 2 +- .../comet/CometSearchProtocolFactory.java | 2 +- .../ms2/pipeline/comet/CometSearchTask.java | 2 +- .../labkey/ms2/pipeline/comet/LegacyCometRun.java | 2 +- .../ms2/pipeline/comet/setCometDefaults.jsp | 2 +- .../pipeline/mascot/MascotCPipelineProvider.java | 2 +- .../ms2/pipeline/mascot/MascotClientImpl.java | 2 +- .../labkey/ms2/pipeline/mascot/MascotConfig.java | 2 +- .../pipeline/mascot/MascotImportPipelineJob.java | 2 +- .../ms2/pipeline/mascot/MascotPipelineJob.java | 2 +- .../org/labkey/ms2/pipeline/mascot/MascotRun.java | 2 +- .../ms2/pipeline/mascot/MascotSearchProtocol.java | 2 +- .../mascot/MascotSearchProtocolFactory.java | 2 +- .../ms2/pipeline/mascot/MascotSearchTask.java | 2 +- .../ms2/pipeline/mascot/setMascotDefaults.jsp | 2 +- .../org/labkey/ms2/pipeline/peaks/PeaksRun.java | 2 +- .../org/labkey/ms2/pipeline/phenyx/PhenyxRun.java | 2 +- .../AbstractMultipleValueParamsValidator.java | 2 +- .../pipeline/sequest/AbstractSequestParams.java | 2 +- .../sequest/AbstractSequestSearchTaskFactory.java | 2 +- .../pipeline/sequest/BooleanParamsValidator.java | 2 +- .../ms2/pipeline/sequest/ConverterFactory.java | 2 +- .../ms2/pipeline/sequest/IInputXMLConverter.java | 2 +- .../ms2/pipeline/sequest/IParamsValidator.java | 2 +- .../ms2/pipeline/sequest/ListParamsValidator.java | 2 +- .../sequest/MultipleDoubleParamsValidator.java | 2 +- .../sequest/MultipleIntegerParamsValidator.java | 2 +- .../pipeline/sequest/Mzxml2SearchConverter.java | 2 +- .../ms2/pipeline/sequest/Mzxml2SearchParam.java | 2 +- .../ms2/pipeline/sequest/Mzxml2SearchParams.java | 2 +- .../sequest/NaturalNumberParamsValidator.java | 2 +- .../NonNegativeIntegerParamsValidator.java | 2 +- .../ms2/pipeline/sequest/Out2XmlConverter.java | 2 +- .../ms2/pipeline/sequest/Out2XmlParams.java | 2 +- .../org/labkey/ms2/pipeline/sequest/Param.java | 2 +- .../org/labkey/ms2/pipeline/sequest/Params.java | 2 +- .../pipeline/sequest/ParamsValidatorFactory.java | 2 +- .../sequest/PositiveDoubleParamsValidator.java | 2 +- .../sequest/RealNumberParamsValidator.java | 2 +- .../pipeline/sequest/SequestBasicConverter.java | 2 +- .../pipeline/sequest/SequestEnzymeConverter.java | 2 +- .../pipeline/sequest/SequestHeaderConverter.java | 2 +- .../labkey/ms2/pipeline/sequest/SequestParam.java | 2 +- .../ms2/pipeline/sequest/SequestParams.java | 2 +- .../pipeline/sequest/SequestParamsBuilder.java | 2 +- .../pipeline/sequest/SequestParamsException.java | 2 +- .../ms2/pipeline/sequest/SequestPipelineJob.java | 2 +- .../pipeline/sequest/SequestPipelineProvider.java | 2 +- .../labkey/ms2/pipeline/sequest/SequestRun.java | 2 +- .../pipeline/sequest/SequestSearchProtocol.java | 2 +- .../sequest/SequestSearchProtocolFactory.java | 2 +- .../ms2/pipeline/sequest/SequestSearchTask.java | 2 +- .../sequest/ThermoSequestParamsBuilder.java | 2 +- .../ms2/pipeline/sequest/setSequestDefaults.jsp | 2 +- .../org/labkey/ms2/pipeline/tandem/XCometRun.java | 2 +- .../ms2/pipeline/tandem/XTandemPipelineJob.java | 2 +- .../pipeline/tandem/XTandemPipelineProvider.java | 2 +- .../labkey/ms2/pipeline/tandem/XTandemRun.java | 2 +- .../pipeline/tandem/XTandemSearchProtocol.java | 2 +- .../tandem/XTandemSearchProtocolFactory.java | 2 +- .../ms2/pipeline/tandem/XTandemSearchTask.java | 2 +- .../ms2/pipeline/tandem/XTandemToXMLTask.java | 2 +- .../ms2/pipeline/tandem/XTandemcometRun.java | 2 +- .../ms2/pipeline/tandem/setTandemDefaults.jsp | 2 +- ms2/src/org/labkey/ms2/protein.jsp | 2 +- ms2/src/org/labkey/ms2/protein/Protein.java | 2 +- .../org/labkey/ms2/protein/ProteinViewBean.java | 15 +++++++++++++++ .../protein/tools/GOPieSectionLabelGenerator.java | 2 +- .../ms2/protein/tools/GOPieToolTipGenerator.java | 2 +- .../ms2/protein/tools/GOPieURLGenerator.java | 2 +- .../org/labkey/ms2/protein/tools/GoHelpers.java | 15 +++++++++++++++ .../labkey/ms2/protein/tools/JChartHelper.java | 2 +- .../ms2/protein/tools/NullOutputStream.java | 2 +- .../labkey/ms2/protein/tools/PieJChartHelper.java | 2 +- .../ms2/protein/tools/ProteinPieDataset.java | 2 +- .../org/labkey/ms2/proteinCoverageMapHeader.jsp | 2 +- ms2/src/org/labkey/ms2/proteinDisambiguation.jsp | 2 +- ms2/src/org/labkey/ms2/proteinSequence.jsp | 2 +- .../ms2/query/AbstractQueryCrosstabView.java | 2 +- .../labkey/ms2/query/ComparePeptideTableInfo.java | 2 +- .../ms2/query/CompareProteinProphetTableInfo.java | 2 +- .../labkey/ms2/query/ComparisonCrosstabView.java | 2 +- .../labkey/ms2/query/FastaRunMappingTable.java | 2 +- ms2/src/org/labkey/ms2/query/FilterView.java | 2 +- .../ms2/query/ITraqProteinQuantitationTable.java | 2 +- ms2/src/org/labkey/ms2/query/MS2Schema.java | 2 +- .../NormalizedProteinProphetCrosstabView.java | 2 +- .../query/PeptideAggregrationDisplayColumn.java | 2 +- .../ms2/query/PeptideCountCoverageColumn.java | 2 +- .../org/labkey/ms2/query/PeptideCrosstabView.java | 2 +- .../org/labkey/ms2/query/PeptidesTableInfo.java | 2 +- .../labkey/ms2/query/ProteinGroupTableInfo.java | 2 +- .../ms2/query/ProteinProphetCrosstabView.java | 2 +- .../ms2/query/ProteinProphetFileTableInfo.java | 2 +- .../ms2/query/ProteinQuantitationTable.java | 2 +- .../labkey/ms2/query/QueryAACoverageColumn.java | 2 +- ms2/src/org/labkey/ms2/query/RunTableInfo.java | 2 +- .../ms2/query/SpectraCountConfiguration.java | 2 +- .../labkey/ms2/query/SpectraCountTableInfo.java | 2 +- .../query/UniquePeptideCountCoverageColumn.java | 2 +- .../labkey/ms2/reader/AbstractMzxmlIterator.java | 2 +- .../org/labkey/ms2/reader/DatDocumentParser.java | 2 +- .../org/labkey/ms2/reader/MGFDocumentParser.java | 2 +- ms2/src/org/labkey/ms2/reader/MS2Loader.java | 2 +- .../labkey/ms2/reader/MS2ModificationList.java | 2 +- ms2/src/org/labkey/ms2/reader/MS2XmlLoader.java | 2 +- .../org/labkey/ms2/reader/MascotDatLoader.java | 2 +- .../org/labkey/ms2/reader/MzMLDocumentParser.java | 2 +- .../labkey/ms2/reader/MzXMLDocumentParser.java | 2 +- ms2/src/org/labkey/ms2/reader/PepXmlLoader.java | 2 +- .../labkey/ms2/reader/PeptideProphetHandler.java | 2 +- .../labkey/ms2/reader/PeptideProphetSummary.java | 2 +- ms2/src/org/labkey/ms2/reader/ProtXmlReader.java | 2 +- ms2/src/org/labkey/ms2/reader/ProteinGroup.java | 2 +- .../org/labkey/ms2/reader/Q3AnalysisSummary.java | 2 +- ms2/src/org/labkey/ms2/reader/Q3Handler.java | 2 +- .../ms2/reader/RandomAccessJrapMzxmlIterator.java | 2 +- .../reader/RandomAccessMzxmlIteratorFactory.java | 2 +- ms2/src/org/labkey/ms2/reader/Rounder.java | 2 +- .../org/labkey/ms2/reader/SensitivitySummary.java | 2 +- .../ms2/reader/SequentialMzxmlIterator.java | 2 +- .../ms2/reader/SequestLogDocumentParser.java | 2 +- .../org/labkey/ms2/reader/SimpleScanIterator.java | 2 +- .../labkey/ms2/reader/SimpleXMLEventRewriter.java | 2 +- ms2/src/org/labkey/ms2/reader/TarIterator.java | 2 +- .../labkey/ms2/reader/XPressAnalysisSummary.java | 2 +- ms2/src/org/labkey/ms2/reader/XPressHandler.java | 2 +- ms2/src/org/labkey/ms2/renameRun.jsp | 2 +- ms2/src/org/labkey/ms2/runSummary.jsp | 2 +- ms2/src/org/labkey/ms2/saveView.jsp | 2 +- ms2/src/org/labkey/ms2/search/peptidePanel.jsp | 2 +- ms2/src/org/labkey/ms2/showPeptide.jsp | 2 +- .../org/labkey/ms2/showPeptideProphetDetails.jsp | 2 +- .../org/labkey/ms2/showPeptideQuantitation.jsp | 2 +- ms2/src/org/labkey/ms2/showProteinGroup.jsp | 2 +- ms2/src/org/labkey/ms2/showSensitivityDetails.jsp | 2 +- ms2/src/org/labkey/ms2/testMascot.jsp | 2 +- .../test/ms2/AbstractMS2SearchEngineTest.java | 2 +- .../org/labkey/test/ms2/AbstractXTandemTest.java | 2 +- .../org/labkey/test/ms2/MS2PipelineFolder.java | 2 +- ms2/test/src/org/labkey/test/ms2/MS2TestBase.java | 2 +- .../src/org/labkey/test/ms2/QuantitationTest.java | 2 +- .../test/ms2/params/MS2EmailSuccessParams.java | 2 +- .../org/labkey/test/ms2/params/MS2TestParams.java | 2 +- .../labkey/test/pages/ms2/MascotConfigPage.java | 2 +- .../org/labkey/test/pages/ms2/MascotTestPage.java | 2 +- .../test/tests/ms2/AbstractMS2ImportTest.java | 2 +- .../src/org/labkey/test/tests/ms2/CometTest.java | 2 +- .../src/org/labkey/test/tests/ms2/LibraTest.java | 2 +- .../org/labkey/test/tests/ms2/MS2ExportTest.java | 2 +- .../labkey/test/tests/ms2/MS2ExtensionsTest.java | 2 +- .../src/org/labkey/test/tests/ms2/MS2GZTest.java | 2 +- .../src/org/labkey/test/tests/ms2/MS2Test.java | 2 +- .../src/org/labkey/test/tests/ms2/MascotTest.java | 2 +- .../src/org/labkey/test/tests/ms2/PeaksTest.java | 2 +- .../org/labkey/test/tests/ms2/PipelineTest.java | 2 +- .../labkey/test/tests/ms2/SequestImportTest.java | 2 +- .../labkey/test/tests/ms2/XTandemShortTest.java | 2 +- .../org/labkey/test/tests/ms2/XTandemTest.java | 2 +- .../test/utils/ms2/Ms2DataRegionExportHelper.java | 2 +- ms2/webapp/MS2/inlineViewDesigner.js | 2 +- .../dbscripts/postgresql/nab-0.000-22.000.sql | 2 +- .../dbscripts/sqlserver/nab-0.000-22.000.sql | 2 +- nab/resources/schemas/nab.xml | 2 +- nab/src/org/labkey/nab/AbstractNabManager.java | 2 +- nab/src/org/labkey/nab/GetNabRunsAction.java | 2 +- nab/src/org/labkey/nab/GetNabRunsBaseForm.java | 2 +- .../org/labkey/nab/GetStudyNabGraphURLAction.java | 2 +- nab/src/org/labkey/nab/GetStudyNabRunsAction.java | 2 +- nab/src/org/labkey/nab/NabAssayController.java | 2 +- nab/src/org/labkey/nab/NabAssayProvider.java | 2 +- nab/src/org/labkey/nab/NabAssayRun.java | 2 +- nab/src/org/labkey/nab/NabContainerListener.java | 2 +- nab/src/org/labkey/nab/NabDataHandler.java | 2 +- nab/src/org/labkey/nab/NabManager.java | 2 +- nab/src/org/labkey/nab/NabModule.java | 2 +- nab/src/org/labkey/nab/NabPlateLayoutHandler.java | 2 +- nab/src/org/labkey/nab/NabRunPropertyMap.java | 2 +- nab/src/org/labkey/nab/NabRunUploadForm.java | 2 +- nab/src/org/labkey/nab/NabUploadWizardAction.java | 2 +- .../labkey/nab/NabVirusFilePropertyHelper.java | 2 +- .../org/labkey/nab/NabVirusPropertyHelper.java | 2 +- nab/src/org/labkey/nab/PlateParserTests.java | 2 +- .../org/labkey/nab/SinglePlateNabAssayRun.java | 2 +- .../org/labkey/nab/SinglePlateNabDataHandler.java | 2 +- nab/src/org/labkey/nab/StudyNabGraphAction.java | 2 +- .../CrossPlateDilutionNabAssayProvider.java | 2 +- .../multiplate/CrossPlateDilutionNabAssayRun.java | 2 +- .../CrossPlateDilutionNabDataHandler.java | 2 +- .../HighThroughputNabAssayProvider.java | 2 +- .../multiplate/HighThroughputNabDataHandler.java | 2 +- .../SinglePlateDilutionNabAssayProvider.java | 2 +- .../SinglePlateDilutionNabAssayRun.java | 2 +- .../SinglePlateDilutionNabDataHandler.java | 2 +- .../SinglePlateDilutionSamplePropertyHelper.java | 2 +- nab/src/org/labkey/nab/query/NabBaseTable.java | 2 +- .../nab/query/NabControlAggregatesTable.java | 15 +++++++++++++++ .../labkey/nab/query/NabDilutionDataTable.java | 2 +- .../org/labkey/nab/query/NabProtocolSchema.java | 2 +- .../org/labkey/nab/query/NabProviderSchema.java | 2 +- nab/src/org/labkey/nab/query/NabRunDataTable.java | 2 +- .../org/labkey/nab/query/NabVirusDataTable.java | 2 +- .../org/labkey/nab/query/NabVirusDomainKind.java | 2 +- .../org/labkey/nab/query/NabWellDataTable.java | 2 +- nab/src/org/labkey/nab/view/nabQC.jsp | 2 +- .../org/labkey/api/protein/CoverageProtein.java | 15 +++++++++++++++ .../org/labkey/api/protein/CoverageViewBean.java | 15 +++++++++++++++ .../api-src/org/labkey/api/protein/MassType.java | 2 +- .../org/labkey/api/protein/MatchCriteria.java | 15 +++++++++++++++ .../labkey/api/protein/PeptideCharacteristic.java | 15 +++++++++++++++ .../org/labkey/api/protein/PeptideUtils.java | 15 +++++++++++++++ .../org/labkey/api/protein/ProteinFeature.java | 15 +++++++++++++++ .../org/labkey/api/protein/ProteinManager.java | 15 +++++++++++++++ .../org/labkey/api/protein/ProteinPlus.java | 2 +- .../org/labkey/api/protein/ProteinSchema.java | 15 +++++++++++++++ .../org/labkey/api/protein/ProteinService.java | 2 +- .../org/labkey/api/protein/ProteomicsModule.java | 2 +- .../api/protein/ProteomicsWebPartFactory.java | 2 +- .../api-src/org/labkey/api/protein/Replicate.java | 15 +++++++++++++++ .../org/labkey/api/protein/SimpleProtein.java | 15 +++++++++++++++ .../protein/annotation/AnnotationInsertion.java | 2 +- .../api/protein/annotation/AnnotationView.java | 2 +- .../annotation/CustomAnnotationImportHelper.java | 2 +- .../protein/annotation/CustomAnnotationSet.java | 2 +- .../annotation/CustomAnnotationSetManager.java | 15 +++++++++++++++ .../protein/annotation/CustomAnnotationType.java | 2 +- .../annotation/DefaultAnnotationLoader.java | 2 +- .../api/protein/annotation/IdentifierType.java | 2 +- .../api/protein/annotation/ProtSprotOrgMap.java | 2 +- .../ProteinAnnotationPipelineProvider.java | 2 +- .../api/protein/annotation/REProperties.java | 2 +- .../api/protein/annotation/XMLProteinHandler.java | 2 +- .../api/protein/annotation/XMLProteinLoader.java | 2 +- .../labkey/api/protein/fasta/FastaDbHelper.java | 2 +- .../labkey/api/protein/fasta/FastaDbLoader.java | 2 +- .../org/labkey/api/protein/fasta/FastaFile.java | 2 +- .../api/protein/fasta/FastaParsingForm.java | 15 +++++++++++++++ .../labkey/api/protein/fasta/FastaProtein.java | 2 +- .../api/protein/fasta/FastaReloaderJob.java | 2 +- .../labkey/api/protein/fasta/FastaValidator.java | 2 +- .../org/labkey/api/protein/fasta/IdPattern.java | 2 +- .../labkey/api/protein/fasta/PeptideHelpers.java | 2 +- .../api/protein/fasta/ProteinFastaLoader.java | 2 +- .../org/labkey/api/protein/go/GoLoader.java | 2 +- .../api/protein/organism/GuessOrgByParsing.java | 2 +- .../protein/organism/GuessOrgBySharedHash.java | 2 +- .../protein/organism/GuessOrgBySharedIdents.java | 2 +- .../org/labkey/api/protein/organism/Organism.java | 2 +- .../protein/organism/OrganismGuessStrategy.java | 2 +- .../org/labkey/api/protein/organism/Timer.java | 2 +- .../api/protein/query/CustomAnnotationSchema.java | 2 +- .../protein/query/CustomAnnotationSetsTable.java | 2 +- .../api/protein/query/CustomAnnotationTable.java | 2 +- .../api/protein/query/OrganismTableInfo.java | 2 +- .../api/protein/query/ProteinUserSchema.java | 2 +- .../api/protein/query/SequencesTableInfo.java | 2 +- .../api/protein/search/MSSearchWebpart.java | 2 +- .../labkey/api/protein/search/PepSearchModel.java | 2 +- .../labkey/api/protein/search/PeptideFilter.java | 2 +- .../protein/search/PeptideFilterSearchForm.java | 15 +++++++++++++++ .../api/protein/search/PeptideSearchForm.java | 15 +++++++++++++++ .../api/protein/search/PeptideSequenceFilter.java | 2 +- .../search/ProbabilityProteinSearchForm.java | 15 +++++++++++++++ .../api/protein/search/ProphetFilterType.java | 15 +++++++++++++++ .../api/protein/search/ProteinSearchBean.java | 2 +- .../api/protein/search/ProteinSearchForm.java | 15 +++++++++++++++ .../api/protein/search/ProteinSearchWebPart.java | 2 +- .../protein/uniprot/CharactersParseActions.java | 2 +- .../labkey/api/protein/uniprot/ParseActions.java | 2 +- .../labkey/api/protein/uniprot/ParseContext.java | 2 +- .../labkey/api/protein/uniprot/ParserTree.java | 2 +- .../api/protein/uniprot/UniprotAnnotation.java | 2 +- .../api/protein/uniprot/UniprotIdentifier.java | 2 +- .../api/protein/uniprot/UniprotOrganism.java | 2 +- .../api/protein/uniprot/UniprotSequence.java | 2 +- .../org/labkey/api/protein/uniprot/uniprot.java | 2 +- .../labkey/api/protein/uniprot/uniprot_entry.java | 2 +- .../protein/uniprot/uniprot_entry_accession.java | 2 +- .../uniprot/uniprot_entry_dbReference.java | 2 +- .../uniprot_entry_dbReference_property.java | 2 +- .../protein/uniprot/uniprot_entry_feature.java | 2 +- .../uniprot_entry_feature_location_begin.java | 2 +- .../uniprot_entry_feature_location_end.java | 2 +- .../protein/uniprot/uniprot_entry_gene_name.java | 2 +- .../protein/uniprot/uniprot_entry_keyword.java | 2 +- .../api/protein/uniprot/uniprot_entry_name.java | 2 +- .../protein/uniprot/uniprot_entry_organism.java | 2 +- .../uniprot_entry_organism_dbReference.java | 2 +- .../uniprot/uniprot_entry_organism_name.java | 2 +- .../uniprot/uniprot_entry_protein_name.java | 2 +- .../uniprot_entry_protein_recommendedName.java | 2 +- ...ot_entry_protein_recommendedName_fullName.java | 2 +- ...t_entry_protein_recommendedName_shortName.java | 2 +- .../protein/uniprot/uniprot_entry_sequence.java | 2 +- .../dbscripts/postgresql/prot-0.000-25.000.sql | 2 +- .../dbscripts/postgresql/prot-25.000-25.001.sql | 5 +++++ .../dbscripts/postgresql/prot-25.002-25.003.sql | 5 +++++ .../dbscripts/sqlserver/prot-0.000-25.000.sql | 2 +- .../dbscripts/sqlserver/prot-25.000-25.001.sql | 5 +++++ .../dbscripts/sqlserver/prot-25.001-25.002.sql | 5 +++++ .../dbscripts/sqlserver/prot-25.002-25.003.sql | 5 +++++ protein/resources/schemas/prot.xml | 2 +- .../org/labkey/protein/CustomProteinListView.java | 2 +- .../labkey/protein/ProteinContainerListener.java | 2 +- .../src/org/labkey/protein/ProteinController.java | 2 +- protein/src/org/labkey/protein/ProteinModule.java | 2 +- .../org/labkey/protein/ProteinServiceImpl.java | 2 +- .../org/labkey/protein/SetBestNameRunnable.java | 2 +- .../src/org/labkey/protein/view/PepSearchView.jsp | 2 +- .../org/labkey/protein/view/annotLoadDetails.jsp | 2 +- .../src/org/labkey/protein/view/insertAnnots.jsp | 2 +- .../org/labkey/protein/view/loadGoAutomatic.jsp | 2 +- .../src/org/labkey/protein/view/loadGoManual.jsp | 2 +- .../org/labkey/protein/view/msTabbedSearch.jsp | 2 +- .../src/org/labkey/protein/view/protAnnots.jsp | 2 +- .../labkey/protein/view/proteinCoverageMap.jsp | 2 +- .../org/labkey/protein/view/searchProteins.jsp | 2 +- .../labkey/protein/view/searchProteinsNarrow.jsp | 2 +- .../org/labkey/protein/view/testFastaParsing.jsp | 2 +- .../view/uploadCustomProteinAnnotations.jsp | 2 +- .../webapp/protein/PeptideCharacteristicLegend.js | 5 +++++ protein/webapp/protein/ProteinCoverageMap.js | 5 +++++ .../assay/signalData/queries/Data.query.xml | 2 +- .../signalData/queries/SearchSignalDataData.sql | 2 +- .../postgresql/signaldata-25.000-25.001.sql | 5 +++++ .../web/signaldata/QCView/DataService.js | 2 +- .../web/signaldata/QCView/ProvisionalRun.js | 2 +- .../web/signaldata/QCView/QualityControl.js | 2 +- .../web/signaldata/QCView/SampleCreator.js | 2 +- .../web/signaldata/QCView/SpectrumPlot.js | 2 +- .../resources/web/signaldata/QCView/Stats.js | 2 +- .../resources/web/signaldata/QCView/signaldata.js | 2 +- .../web/signaldata/ResultUpdate/resultupdate.js | 2 +- .../web/signaldata/UploadView/UploadLog.js | 2 +- .../signaldata/UploadView/uploadResultDataForm.js | 2 +- .../signaldata/UploadView/uploadResultFiles.js | 2 +- .../labkey/signaldata/SignalDataController.java | 2 +- .../org/labkey/signaldata/SignalDataModule.java | 2 +- .../labkey/signaldata/SignalDataUpgradeCode.java | 15 +++++++++++++++ .../assay/SignalDataAssayDataHandler.java | 2 +- .../signaldata/SignalDataAssayBeginPage.java | 2 +- .../pages/signaldata/SignalDataRunViewerPage.java | 2 +- .../pages/signaldata/SignalDataUploadPage.java | 2 +- .../test/tests/signaldata/SignalDataRawTest.java | 2 +- .../util/signaldata/SignalDataInitializer.java | 2 +- .../dbscripts/postgresql/viability-0.00-16.10.sql | 2 +- .../postgresql/viability-25.000-25.001.sql | 5 +++++ .../org/labkey/viability/GuavaDataHandler.java | 2 +- .../viability/ViabilityAssayDataHandler.java | 2 +- .../labkey/viability/ViabilityAssayProvider.java | 2 +- .../viability/ViabilityAssayRunUploadForm.java | 2 +- .../labkey/viability/ViabilityAssaySchema.java | 2 +- .../ViabilityAssayUploadWizardAction.java | 2 +- .../org/labkey/viability/ViabilityController.java | 2 +- .../viability/ViabilityDataExchangeHandler.java | 2 +- .../org/labkey/viability/ViabilityManager.java | 2 +- .../src/org/labkey/viability/ViabilityModule.java | 2 +- .../src/org/labkey/viability/ViabilityResult.java | 2 +- .../ViabilitySpecimenChangeListener.java | 2 +- .../labkey/viability/ViabilityTsvDataHandler.java | 2 +- .../viability/data/MultiValueInputColumn.java | 2 +- viability/webapp/viability/MultiValueInput.js | 2 +- 976 files changed, 1721 insertions(+), 901 deletions(-) diff --git a/elisa/jest.config.js b/elisa/jest.config.js index cca2fded7b..f7fe5d222c 100644 --- a/elisa/jest.config.js +++ b/elisa/jest.config.js @@ -1,3 +1,8 @@ +/* + * Copyright (c) 2025-2026 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0 + */ module.exports = { globals: { LABKEY: { diff --git a/elisa/resources/schemas/dbscripts/postgresql/elisa-0.000-23.000.sql b/elisa/resources/schemas/dbscripts/postgresql/elisa-0.000-23.000.sql index 0cab65f486..3198655693 100644 --- a/elisa/resources/schemas/dbscripts/postgresql/elisa-0.000-23.000.sql +++ b/elisa/resources/schemas/dbscripts/postgresql/elisa-0.000-23.000.sql @@ -1,5 +1,5 @@ /* - * Copyright (c) 2020 LabKey Corporation + * Copyright (c) 2020-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/elisa/resources/schemas/dbscripts/sqlserver/elisa-0.000-23.000.sql b/elisa/resources/schemas/dbscripts/sqlserver/elisa-0.000-23.000.sql index a5d686383c..8aab5fa3cf 100644 --- a/elisa/resources/schemas/dbscripts/sqlserver/elisa-0.000-23.000.sql +++ b/elisa/resources/schemas/dbscripts/sqlserver/elisa-0.000-23.000.sql @@ -1,5 +1,5 @@ /* - * Copyright (c) 2020 LabKey Corporation + * Copyright (c) 2020-2026 LabKey Corporation * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/elisa/resources/schemas/elisa.xml b/elisa/resources/schemas/elisa.xml index 2796a6e97e..205056fa0b 100644 --- a/elisa/resources/schemas/elisa.xml +++ b/elisa/resources/schemas/elisa.xml @@ -1,7 +1,7 @@